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Al-Jawabreh R, Lastik D, McKenzie D, Reynolds K, Suleiman M, Mousley A, Atkinson L, Hunt V. Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220437. [PMID: 38008117 PMCID: PMC10676819 DOI: 10.1098/rstb.2022.0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 11/28/2023] Open
Abstract
Among nematodes, the free-living model organism Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Reem Al-Jawabreh
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Dominika Lastik
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | - Kieran Reynolds
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Mona Suleiman
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | | | - Vicky Hunt
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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2
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McClure CR, Patel R, Hallem EA. Invade or die: behaviours and biochemical mechanisms that drive skin penetration in Strongyloides and other skin-penetrating nematodes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220434. [PMID: 38008119 PMCID: PMC10676818 DOI: 10.1098/rstb.2022.0434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/05/2023] [Indexed: 11/28/2023] Open
Abstract
Skin-penetrating nematodes, including the human threadworm Strongyloides stercoralis and hookworms in the genera Necator and Ancylostoma, are gastrointestinal parasites that are a major cause of neglected tropical disease in low-resource settings worldwide. These parasites infect hosts as soil-dwelling infective larvae that navigate towards hosts using host-emitted sensory cues such as odorants and body heat. Upon host contact, they invade the host by penetrating through the skin. The process of skin penetration is critical for successful parasitism but remains poorly understood and understudied. Here, we review current knowledge of skin-penetration behaviour and its underlying mechanisms in the human parasite S. stercoralis, the closely related rat parasite Strongyloides ratti, and other skin-penetrating nematodes such as hookworms. We also highlight important directions for future investigations into this underexplored process and discuss how recent advances in molecular genetic and genomic tools for Strongyloides species will enable mechanistic investigations of skin penetration and other essential parasitic behaviours in future studies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Courtney R. McClure
- Molecular Toxicology Interdepartmental PhD Program, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Ruhi Patel
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Elissa A. Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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Alipour M, Masoori L, Gholami MD, Khoshmirsafa M, Razmjou E, Jalallou N, Jafarian F, Falak R, Meamar AR. Expression of Heat Shock Protein 70 (HSP70) and Astacin Genes of Strongyloides stercoralis as well as HSP70 and HSP17.1 Genes of S. ratti in Adult and Larval Stages of S. stercoralis. IRANIAN JOURNAL OF PARASITOLOGY 2024; 19:1-8. [PMID: 38654956 PMCID: PMC11033530 DOI: 10.18502/ijpa.v19i1.15187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/14/2023] [Indexed: 04/26/2024]
Abstract
Background Uncovering the roles and characteristics of pathogenesis-related molecules can help us develop novel management methods in parasitology. In this study, we studied the expression levels of Strongyloides stercoralis heat shock protein70 (HSP70) (Sst-hsp-70) and astacin (Sst-ast) as pathogenesis-related genes as well as the expression of S. ratti HSP70 and HSP17.1 (Sra-hsp-70, Sra-hsp-17.1) in the larvae and adult stages of S. stercoralis. Methods A hyperinfection isolate of S. stercoralis from Gilan Province, northern Iran was cultivated on nutrient agar. After a couple of days, parasites in different stages of life were collected, and total RNA was extracted. The expression levels of astacin and HSP genes were compared by real-time PCR. Results Statistically higher expression levels of Sst-ast, Sst-hsp-70, and Sra-hsp-70 genes in L3 larvae than in adults were observed. However, the expression level of Sra-hsp-17.1 was non-significantly lower in the larval stage than in adult worms. Conclusion Higher expression levels of Sst-ast, Sst-hsp-70, and Sra-hsp-70 genes in the larval stages of S. stercoralis suggest the potential role of these enzymes in parasite cutaneous invasion and pathogenesis. However, higher expression of Srahsp-17.1 in adult forms is probably involved in resistance and survival mechanisms. The similarity in gene expression between S. stercoralis and S. ratti can provide helpful hints to better understand strongyloidiasis from various perspectives, including pathogenesis, proper diagnosis, and targeted treatment.
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Affiliation(s)
- Maryam Alipour
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Leila Masoori
- Department of Laboratory Sciences, School of Allied Medical Sciences, Lorestan University of Medical Sciences, Khorramabad, Iran
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohammad Davoodzadeh Gholami
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Khoshmirsafa
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Elham Razmjou
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nahid Jalallou
- Department of Medical Laboratory Science, AJA University of Medical Sciences, Tehran, Iran
| | - Farzane Jafarian
- Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Mazandaran, Iran
| | - Reza Falak
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Meamar
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Maciejowski WJ, Gile GH, Jerlström-Hultqvist J, Dacks JB. Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia. Int J Parasitol 2023; 53:233-245. [PMID: 36898426 DOI: 10.1016/j.ijpara.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
The eukaryotic phylum Parabasalia is composed primarily of anaerobic, endobiotic organisms such as the veterinary parasite Tritrichomonas foetus and the human parasite Trichomonas vaginalis, the latter causing the most prevalent, non-viral, sexually transmitted disease world-wide. Although a parasitic lifestyle is generally associated with a reduction in cell biology, T. vaginalis provides a striking counter-example. The 2007 T. vaginalis genome paper reported a massive and selective expansion of encoded proteins involved in vesicle trafficking, particularly those implicated in the late secretory and endocytic systems. Chief amongst these were the hetero-tetrameric adaptor proteins or 'adaptins', with T. vaginalis encoding ∼3.5 times more such proteins than do humans. The provenance of such a complement, and how it relates to the transition from a free-living or endobiotic state to parasitism, remains unclear. In this study, we performed a comprehensive bioinformatic and molecular evolutionary investigation of the heterotetrameric cargo adaptor-derived coats, comparing the molecular complement and evolution of these proteins between T. vaginalis, T. foetus and the available diversity of endobiotic parabasalids. Notably, with the recent discovery of Anaeramoeba spp. as the free-living sister lineage to all parabasalids, we were able to delve back to time points earlier in the lineage's history than ever before. We found that, although T. vaginalis still encodes the most HTAC subunits amongst parabasalids, the duplications giving rise to the complement took place more deeply and at various stages across the lineage. While some duplications appear to have convergently shaped the parasitic lineages, the largest jump is in the transition from free-living to endobiotic lifestyle with both gains and losses shaping the encoded complement. This work details the evolution of a cellular system across an important lineage of parasites and provides insight into the evolutionary dynamics of an example of expansion of protein machinery, counter to the more common trends observed in many parasitic systems.
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Affiliation(s)
- William J Maciejowski
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, Arizona, USA
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Box 586, Uppsala Universitet, SE-751 24 Uppsala, Sweden. https://twitter.com/jon_hultqvist
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
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Verhoeven A, Finkers-Tomczak A, Prins P, Valkenburg-van Raaij DR, van Schaik CC, Overmars H, van Steenbrugge JJM, Tacken W, Varossieau K, Slootweg EJ, Kappers IF, Quentin M, Goverse A, Sterken MG, Smant G. The root-knot nematode effector MiMSP32 targets host 12-oxophytodienoate reductase 2 to regulate plant susceptibility. THE NEW PHYTOLOGIST 2023; 237:2360-2374. [PMID: 36457296 DOI: 10.1111/nph.18653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
To establish persistent infections in host plants, herbivorous invaders, such as root-knot nematodes, must rely on effectors for suppressing damage-induced jasmonate-dependent host defenses. However, at present, the effector mechanisms targeting the biosynthesis of biologically active jasmonates to avoid adverse host responses are unknown. Using yeast two-hybrid, in planta co-immunoprecipitation, and mutant analyses, we identified 12-oxophytodienoate reductase 2 (OPR2) as an important host target of the stylet-secreted effector MiMSP32 of the root-knot nematode Meloidogyne incognita. MiMSP32 has no informative sequence similarities with other functionally annotated genes but was selected for the discovery of novel effector mechanisms based on evidence of positive, diversifying selection. OPR2 catalyzes the conversion of a derivative of 12-oxophytodienoate to jasmonic acid (JA) and operates parallel to 12-oxophytodienoate reductase 3 (OPR3), which controls the main pathway in the biosynthesis of jasmonates. We show that MiMSP32 targets OPR2 to promote parasitism of M. incognita in host plants independent of OPR3-mediated JA biosynthesis. Artificially manipulating the conversion of the 12-oxophytodienoate by OPRs increases susceptibility to multiple unrelated plant invaders. Our study is the first to shed light on a novel effector mechanism targeting this process to regulate the susceptibility of host plants.
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Affiliation(s)
- Ava Verhoeven
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Plant Stress Resilience, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant-Environment Signaling, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Anna Finkers-Tomczak
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Pjotr Prins
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Debbie R Valkenburg-van Raaij
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Casper C van Schaik
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Joris J M van Steenbrugge
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Wannes Tacken
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Koen Varossieau
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Erik J Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Iris F Kappers
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903, Sophia Antipolis, France
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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Mendez P, Walsh B, Hallem EA. Using newly optimized genetic tools to probe Strongyloides sensory behaviors. Mol Biochem Parasitol 2022; 250:111491. [PMID: 35697205 PMCID: PMC9339661 DOI: 10.1016/j.molbiopara.2022.111491] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
The oft-neglected human-parasitic threadworm, Strongyloides stercoralis, infects roughly eight percent of the global population, placing disproportionate medical and economic burden upon marginalized communities. While current chemotherapies treat strongyloidiasis, disease recrudescence and the looming threat of anthelminthic resistance necessitate novel strategies for nematode control. Throughout its life cycle, S. stercoralis relies upon sensory cues to aid in environmental navigation and coordinate developmental progression. Odorants, tastants, gases, and temperature have been shown to shape parasite behaviors that drive host seeking and infectivity; however, many of these sensory behaviors remain poorly understood, and their underlying molecular and neural mechanisms are largely uncharacterized. Disruption of sensory circuits essential to parasitism presents a promising strategy for future interventions. In this review, we describe our current understanding of sensory behaviors - namely olfactory, gustatory, gas sensing, and thermosensory behaviors - in Strongyloides spp. We also highlight the ever-growing cache of genetic tools optimized for use in Strongyloides that have facilitated these findings, including transgenesis, CRISPR/Cas9-mediated mutagenesis, RNAi, chemogenetic neuronal silencing, and the use of fluorescent biosensors to measure neuronal activity. Bolstered by these tools, we are poised to enter an era of rapid discovery in Strongyloides sensory neurobiology, which has the potential to shape pioneering advances in the prevention and treatment of strongyloidiasis.
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Affiliation(s)
- Patricia Mendez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Interdepartmental PhD Program, University of California Los Angeles, Los Angeles, CA, USA.
| | - Breanna Walsh
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Interdepartmental PhD Program, University of California Los Angeles, Los Angeles, CA, USA; Medical Scientist Training Program, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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Pomari E, Malerba G, Veschetti L, Franceschi A, Moron Dalla Tor L, Deiana M, Degani M, Mistretta M, Patuzzo C, Ragusa A, Mori A, Bisoffi Z, Buonfrate D. Identification of miRNAs of Strongyloides stercoralis L1 and iL3 larvae isolated from human stool. Sci Rep 2022; 12:9957. [PMID: 35705621 PMCID: PMC9200769 DOI: 10.1038/s41598-022-14185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Strongyloidiasis is a neglected tropical disease caused by the soil-transmitted nematode by Strongyloides stercoralis, that affects approximately 600 million people worldwide. In immunosuppressed individuals disseminated strongyloidiasis can rapidly lead to fatal outcomes. There is no gold standard for diagnosing strongyloidiasis, and infections are frequently misdiagnosed. A better understanding of the molecular biology of this parasite can be useful for example for the discovery of potential new biomarkers. Interestingly, recent evidence showed the presence of small RNAs in Strongyloididae, but no data was provided for S. stercoralis. In this study, we present the first identification of miRNAs of both L1 and iL3 larval stages of S. stercoralis. For our purpose, the aims were: (i) to analyse the miRNome of L1 and iL3 S. stercoralis and to identify potential miRNAs of this nematode, (ii) to obtain the mRNAs profiles in these two larval stages and (iii) to predict potential miRNA target sites in mRNA sequences. Total RNA was isolated from L1 and iL3 collected from the stool of 5 infected individuals. For the miRNAs analysis, we used miRDeep2 software and a pipeline of bio-informatic tools to construct a catalog of a total of 385 sequences. Among these, 53% were common to S. ratti, 19% to S. papillosus, 1% to Caenorhabditis elegans and 44% were novel. Using a differential analysis between the larval stages, we observed 6 suggestive modulated miRNAs (STR-MIR-34A-3P, STR-MIR-8397-3P, STR-MIR-34B-3P and STR-MIR-34C-3P expressed more in iL3, and STR-MIR-7880H-5P and STR-MIR-7880M-5P expressed more in L1). Along with this analysis, we obtained also the mRNAs profiles in the same samples of larvae. Multiple testing found 81 statistically significant mRNAs of the total 1553 obtained (FDR < 0.05; 32 genes expressed more in L1 than iL3; 49 genes expressed more in L3 than iL1). Finally, we found 33 predicted mRNA targets of the modulated miRNAs, providing relevant data for a further validation to better understand the role of these small molecules in the larval stages and their valuein clinical diagnostics.
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Affiliation(s)
- Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy.
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Alessandra Franceschi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | | | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Monica Degani
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Dora Buonfrate
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
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Yuan D, Li S, Shang Z, Wan M, Lin Y, Zhang Y, Feng Y, Xu L, Xiao L. Genus-level evolutionary relationships of FAR proteins reflect the diversity of lifestyles of free-living and parasitic nematodes. BMC Biol 2021; 19:178. [PMID: 34461887 PMCID: PMC8407040 DOI: 10.1186/s12915-021-01111-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023] Open
Abstract
Background Nematodes are a widespread and diverse group comprising free-living and parasitic species, some of which have major detrimental effects on crops, animals, and human health. Genomic comparisons of nematodes may help reveal the genetic bases for the evolution of parasitic lifestyles. Fatty acid and retinol-binding proteins (FARs) are thought to be unique to nematodes and play essential roles in their development, reproduction, infection, and possibly parasitism through promoting the uptake, transport, and distribution of lipid and retinol. However, the evolution of FAR family proteins across the phylum Nematoda remains elusive. Results We report here the evolutionary relationship of the FAR gene family across nematodes. No FAR was found in Trichocephalida species and Romanomermis culicivorax from Clade I, and FAR could be found in species from Clades III, IV, and V. FAR proteins are conserved in Clade III species and separated into three clusters. Tandem duplications and high divergence events lead to variable richness and low homology of FARs in Steinernema of Clade IVa, Strongyloides of Clade IVb, and intestinal parasitic nematodes from Clades Vc and Ve. Moreover, different richness and sequence variations of FARs in pine wood, root-knot, stem, and cyst nematodes might be determined by reproduction mode or parasitism. However, murine lungworm Angiostrongylus and bovine lungworm Dictyocaulus viviparus from Clade Vd have only 3–4 orthologs of FAR. RNA-seq data showed that far genes, especially far-1 and far-2, were highly expressed in most nematodes. Angiostrongylus cantonensis FAR-1 and FAR-3 have low sequence homology and distinct ligand-binding properties, leading to differences in the cavity volume of proteins. These data indicate that FAR proteins diverged early and experienced low selective pressure to form genus-level diversity. The far genes are present in endophyte or root-colonized bacteria of Streptomyces, Kitasatospora sp., Bacillus subtilis, and Lysobacter, suggesting that bacterial far genes might be derived from plant-parasitic nematodes by horizontal gene transfer. Conclusions Data from these comparative analyses have provided insights into genus-level diversity of FAR proteins in the phylum Nematoda. FAR diversification provides a glimpse into the complicated evolution history across free-living and parasitic nematodes. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01111-3.
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Affiliation(s)
- Dongjuan Yuan
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Song Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Ziyu Shang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Muchun Wan
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yu Lin
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yanhua Zhang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Lian Xu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, China.
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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9
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Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, Glover N. Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism. Genome Biol Evol 2021; 13:evab010. [PMID: 33484570 PMCID: PMC7936022 DOI: 10.1093/gbe/evab010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2021] [Indexed: 01/10/2023] Open
Abstract
Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host-parasite adaptation.
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Affiliation(s)
- Natalia Zajac
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Stefan Zoller
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Katri Seppälä
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - David Moi
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
- Centre for Life’s Origins and Evolution, Department of Genetics Evolution and Environment, University College London, United Kingdom
- Department of Computer Science, University College London, United Kingdom
| | - Jukka Jokela
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Hanna Hartikainen
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
- School of Life Sciences, University of Nottingham, University Park, United Kingdom
| | - Natasha Glover
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
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10
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Ma X, Xu W, Liu T, Chen R, Zhu H, Zhang H, Cai C, Li S. Functional characterization of soybean (Glycine max) DIRIGENT genes reveals an important role of GmDIR27 in the regulation of pod dehiscence. Genomics 2021; 113:979-990. [PMID: 33144217 DOI: 10.1016/j.ygeno.2020.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/02/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022]
Abstract
DIRIGENT (DIR) genes play important roles in regulating plant growth and development and have been studied in many plant species. However, information on DIR genes in soybean is limited. Here, we identified and characterized 54 GmDIRs and studied the characteristics of GmDIRs. Most of the GmDIRs contained a classical gene structure, one exon; 26 conserved motifs were found among these GmDIRs. The GmDIRs were grouped into four subfamilies, DIR-a, DIR-b, DIR-e and DIR-f, based on a phylogenetic analysis, and 24 duplicated gene pairs were identified. Differences in the cis-acting elements in the GmDIR promoter regions might result in distinct expression patterns of GmDIRs in different tissues. In addition, GmDIR27 had a close relationship with the pod dehiscence gene GmPdh1, and overexpression of GmDIR27 increased pod dehiscence by affecting several pod dehiscence-related gene expressions. Generally, our results provide essential information that aids future efforts to functionally characterize soybean GmDIR genes.
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Affiliation(s)
- Xiaofei Ma
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenying Xu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Tong Liu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Ruying Chen
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Huiying Zhang
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Chunmei Cai
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuai Li
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China.
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Dulovic A, Renahan T, Röseler W, Rödelsperger C, Rose AM, Streit A. Rhabditophanes diutinus a parthenogenetic clade IV nematode with dauer larvae. PLoS Pathog 2020; 16:e1009113. [PMID: 33270811 PMCID: PMC7738172 DOI: 10.1371/journal.ppat.1009113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 12/15/2020] [Accepted: 10/30/2020] [Indexed: 01/13/2023] Open
Abstract
Comparative studies using non-parasitic model species such as Caenorhabditis elegans, have been very helpful in investigating the basic biology and evolution of parasitic nematodes. However, as phylogenetic distance increases, these comparisons become more difficult, particularly when outside of the nematode clade to which C. elegans belongs (V). One of the reasons C. elegans has nevertheless been used for these comparisons, is that closely related well characterized free-living species that can serve as models for parasites of interest are frequently not available. The Clade IV parasitic nematodes Strongyloides are of great research interest due to their life cycle and other unique biological features, as well as their medical and veterinary importance. Rhabditophanes, a closely related free-living genus, forms part of the Strongyloidoidea nematode superfamily. Rhabditophanes diutinus (= R. sp. KR3021) was included in the recent comparative genomic analysis of the Strongyloididae, providing some insight into the genomic nature of parasitism. However, very little is known about this species, limiting its usefulness as a research model. Here we provide a species description, name the species as R. diutinus and investigate its life cycle and subsequently gene expression in multiple life stages. We identified two previously unreported starvation induced life stages: dauer larvae and arrested J2 (J2A) larvae. The dauer larvae are morphologically similar to and are the same developmental stage as dauers in C. elegans and infective larvae in Strongyloides. As in C. elegans and Strongyloides, dauer formation is inhibited by treatment with dafachronic acid, indicating some genetic control mechanisms are conserved. Similarly, the expression patterns of putative dauer/infective larva control genes resemble each other, in particular between R. diutinus and Strongyloides spp. These findings illustrate and increase the usefulness of R. diutinus as a non-parasitic, easy to work with model species for the Strongyloididae for studying the evolution of parasitism as well as many aspects of the biology of Strongyloides spp, in particular the formation of infective larvae. Parasitic worms are an issue of great medical, veterinary, agricultural and economic importance, yet little is known about how worms become parasites. Comparative studies with non-parasitic model species like C. elegans have been useful, however, this usefulness decreases as the evolutionary distance between the species increases. One way to combat this is by having more well-studied closely related species to parasites of interest. To address this, we provide information about Rhabditophanes diutinus, a free-living nematode that is part of the same superfamily as the medically and veterinary important Strongyloides parasites. We provide analysis on its life cycle, in particular on two starvation induced life stages, along with gene expression data. Overall, this important information illustrates and improves the use of R. diutinus, as a non-parasitic model species for studying parasite evolution and basic biology within Strongyloides.
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Affiliation(s)
- Alex Dulovic
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Tess Renahan
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Waltraud Röseler
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Christian Rödelsperger
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Ann M. Rose
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adrian Streit
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
- * E-mail:
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12
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Xu L, Yang J, Xu M, Shan D, Wu Z, Yuan D. Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda. BMC Biol 2020; 18:181. [PMID: 33243226 PMCID: PMC7694339 DOI: 10.1186/s12915-020-00896-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background Nematodes have evolved to survive in diverse ecological niches and can be a serious burden on agricultural economy, veterinary medicine, and public health. Antioxidant enzymes in parasitic nematodes play a critical role in defending against host oxidative stress. However, the features of the evolution of antioxidant enzymes in the phylum Nematoda remain elusive. Results Here, we systematically investigated the evolution and gene expression of antioxidant enzymes in the genomes of 59 nematodes and transcriptomes of 20 nematodes. Catalase has been independently lost in several orders, suggesting that it is unnecessary for some nematodes. Unlike in mammals, phospholipid hydroperoxide glutathione peroxidase is widely distributed in nematodes, among which it has evolved independently. We found that superoxide dismutase (SOD) has been present throughout nematode evolutionary process, and the extracellular isoform (SOD3) is diverged from the corresponding enzyme in mammals and has undergone duplication and differentiation in several nematodes. Moreover, the evolution of intracellular and extracellular SOD isoforms in filaria strongly indicates that extracellular SOD3 originated from intracellular SOD1 and underwent rapid evolution to form the diversity of extracellular SOD3. We identify a novel putative metal-independent extracellular SOD presenting independently in Steinernema and Strongyloididae lineage that featured a high expression level in Strongyloides larvae. Sequence divergence of SOD3 between parasitic nematodes and their closest free-living nematode, the specifically high expression in the parasitic female stage, and presence in excretory-secretory proteome of Strongyloides suggest that SOD3 may be related with parasitism. Conclusions This study advances our understanding of the complex evolution of antioxidant enzymes across Nematoda and provides targets for controlling parasitic nematode diseases.
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Affiliation(s)
- Lian Xu
- Key Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.,Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jian Yang
- Key Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Meng Xu
- Department of Ecology, Jinan University, Guangzhou, 510632, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Dongjuan Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Rojas-Pirela M, Andrade-Alviárez D, Rojas V, Kemmerling U, Cáceres AJ, Michels PA, Concepción JL, Quiñones W. Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. Open Biol 2020; 10:200302. [PMID: 33234025 PMCID: PMC7729029 DOI: 10.1098/rsob.200302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phosphoglycerate kinase (PGK) is a glycolytic enzyme that is well conserved among the three domains of life. PGK is usually a monomeric enzyme of about 45 kDa that catalyses one of the two ATP-producing reactions in the glycolytic pathway, through the conversion of 1,3-bisphosphoglycerate (1,3BPGA) to 3-phosphoglycerate (3PGA). It also participates in gluconeogenesis, catalysing the opposite reaction to produce 1,3BPGA and ADP. Like most other glycolytic enzymes, PGK has also been catalogued as a moonlighting protein, due to its involvement in different functions not associated with energy metabolism, which include pathogenesis, interaction with nucleic acids, tumorigenesis progression, cell death and viral replication. In this review, we have highlighted the overall aspects of this enzyme, such as its structure, reaction kinetics, activity regulation and possible moonlighting functions in different protistan organisms, especially both free-living and parasitic Kinetoplastea. Our analysis of the genomes of different kinetoplastids revealed the presence of open-reading frames (ORFs) for multiple PGK isoforms in several species. Some of these ORFs code for unusually large PGKs. The products appear to contain additional structural domains fused to the PGK domain. A striking aspect is that some of these PGK isoforms are predicted to be catalytically inactive enzymes or ‘dead’ enzymes. The roles of PGKs in kinetoplastid parasites are analysed, and the apparent significance of the PGK gene duplication that gave rise to the different isoforms and their expression in Trypanosoma cruzi is discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Verónica Rojas
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Universidad de Chile, Facultad de Medicina, Santiago de Chile 8380453, Santigo de Chile
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Paul A Michels
- Centre for Immunity, Infection and Evolution, The King's Buildings, Edinburgh EH9 3FL, UK.,Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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Tan JH, Lautens M, Romanelli-Cedrez L, Wang J, Schertzberg MR, Reinl SR, Davis RE, Shepherd JN, Fraser AG, Salinas G. Alternative splicing of coq-2 controls the levels of rhodoquinone in animals. eLife 2020; 9:e56376. [PMID: 32744503 PMCID: PMC7434440 DOI: 10.7554/elife.56376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022] Open
Abstract
Parasitic helminths use two benzoquinones as electron carriers in the electron transport chain. In normoxia, they use ubiquinone (UQ), but in anaerobic conditions inside the host, they require rhodoquinone (RQ) and greatly increase RQ levels. We previously showed the switch from UQ to RQ synthesis is driven by a change of substrates by the polyprenyltransferase COQ-2 (Del Borrello et al., 2019; Roberts Buceta et al., 2019); however, the mechanism of substrate selection is not known. Here, we show helminths synthesize two coq-2 splice forms, coq-2a and coq-2e, and the coq-2e-specific exon is only found in species that synthesize RQ. We show that in Caenorhabditis elegans COQ-2e is required for efficient RQ synthesis and survival in cyanide. Importantly, parasites switch from COQ-2a to COQ-2e as they transit into anaerobic environments. We conclude helminths switch from UQ to RQ synthesis principally via changes in the alternative splicing of coq-2.
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Affiliation(s)
- June H Tan
- The Donnelly Centre, University of TorontoTorontoCanada
| | | | - Laura Romanelli-Cedrez
- Laboratorio de Biología de Gusanos. Unidad Mixta, Departamento de Biociencias, Facultad de Química, Universidad de la República - Institut Pasteur de MontevideoMontevideoUruguay
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Department of Biochemistry and Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | | | - Samantha R Reinl
- Department of Chemistry and Biochemistry, Gonzaga UniversitySpokaneUnited States
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Jennifer N Shepherd
- Department of Chemistry and Biochemistry, Gonzaga UniversitySpokaneUnited States
| | | | - Gustavo Salinas
- Laboratorio de Biología de Gusanos. Unidad Mixta, Departamento de Biociencias, Facultad de Química, Universidad de la República - Institut Pasteur de MontevideoMontevideoUruguay
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Genome-wide identification and characterization of nonspecific lipid transfer protein (nsLTP) genes in Arachis duranensis. Genomics 2020; 112:4332-4341. [PMID: 32717318 DOI: 10.1016/j.ygeno.2020.07.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/07/2020] [Accepted: 07/20/2020] [Indexed: 11/24/2022]
Abstract
Nonspecific lipid transfer proteins (nsLTPs) play vital roles in lipid metabolism, cell apoptosis and biotic and abiotic stresses in plants. However, the distribution of nsLTPs in Arachis duranensis has not been fully characterized. In this study, we identified 64 nsLTP genes in A. duranensis (designated AdLTPs), which were classified into six subfamilies and randomly distributed along nine chromosomes. Tandem and segmental duplication events were detected in the evolution of AdLTPs. The Ks and ω values differed significantly between Types 1 and D subfamilies, and eight AdLTPs were under positive selection. The expression levels of AdLTPs were changed after salinity, PEG, low-temperature and ABA treatments. Three AdLTPs were associated with resistance to nematode infection, and DOF and WRI1 transcription factors may regulate the AdLTP response to nematode infection. Our results may provide valuable genomic information for the breeding of peanut cultivars that are resistant to biotic and abiotic stresses.
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Abstract
Purpose of Review This paper constitutes an update of recent studies on the general biology, molecular genetics, and cellular biology of Strongyloides spp. and related parasitic nematodes. Recent Findings Increasingly, human strongyloidiasis is considered the most neglected of neglected tropical diseases. Despite this, the last 5 years has seen remarkable advances in the molecular biology of Strongyloides spp. Genome sequences for S. stercoralis, S. ratti, S. venezuelensis, S. papillosus, and the related parasite Parastrongyloides trichosuri were created, annotated, and analyzed. These genomic resources, along with a practical transgenesis platform for Strongyloides spp., aided a major achievement, the advent of targeted mutagenesis via CRISPR/Cas9 in S. stercoralis and S. ratti. The genome sequences have also enabled significant molecular epidemiologic and phylogenetic findings on human strongyloidiasis, including the first genetic evidence of zoonotic transmission of S. stercoralis between dogs and humans. Studies of molecular signaling pathways identified the nuclear receptor Ss-DAF-12 as one that can be manipulated in the parasite by exogenous application of its steroid ligands. The chemotherapeutic implications of this were unscored by a study in which a Ss-DAF-12 ligand suppressed autoinfection by S. stercoralis in a new murine model of human strongyloidiasis. Summary Seminal advances in genomics of Strongyloides spp. have transformed research into strongyloidiasis, facilitating fundamental phylogenetic and epidemiologic studies and aiding the deployment of CRISPR/Cas9 gene disruption and editing as functional genomic tools in Strongyloides spp. Studies of Ss-DAF-12 signaling in S. stercoralis demonstrated the potential of this pathway as a novel chemotherapeutic target in parasitic nematodes.
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Affiliation(s)
- Tegegn G. Jaleta
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James B. Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Comparative Genomic Analysis of Trichinella spiralis Reveals Potential Mechanisms of Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2948973. [PMID: 31240209 PMCID: PMC6556364 DOI: 10.1155/2019/2948973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
Trichinellosis caused by parasitic nematodes of the genus Trichinella may result in human morbidity and mortality worldwide. Deciphering processes that drive species diversity and adaptation are key to understanding parasitism and developing effective control strategies. Our goal was to identify genes that are under positive selection and possible mechanisms of adaptive evolution of Trichinella spiralis genes using a comparative genomic analysis with the genomes of Brugia malayi, Trichuris suis, Ancylostoma ceylanicum, and Caenorhabditis elegans. The CODEML program derived from the PAML package was used to deduce the most probable dN/dS ratio, a measurement to detect genes/proteins undergoing adaptation. For each pair of sequences, those with a dN/dS ratio > 1 were considered positively selected genes (PSGs). Altogether, 986 genes were positively selected (p-value < 0.01). Genes involved in metabolic pathways, signaling pathways, and cytosolic DNA-sensing pathways were significantly enriched among the PSGs. Several PSGs are associated with exploitation of the host: modification of the host's metabolism, creation of new parasite-specific morphological structures between T. spiralis and the host interface, xenobiotic metabolism to combat low oxygen concentrations and host toxicity, muscle cell transformation, cell cycle arrest, DNA repair processes during nurse cell formation, antiapoptotic factors, immunomodulation, and regulation of epigenetic processes. Some of the T. spiralis PSGs have C. elegans orthologs that confer severe or lethal RNAi phenotypes. Fifty-seven PSGs in T. spiralis were analyzed to encode differentially expressed proteins. The present study utilized an overall comparative genomic analysis to discover PSGs within T. spiralis and their relationships with biological function and organism fitness. This analysis adds to our understanding of the possible mechanism that contributes to T. spiralis parasitism and biological adaptation within the host, and thus these identified genes may be potential targets for drug and vaccine development.
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18
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Li S, Wang R, Jin H, Ding Y, Cai C. Molecular Characterization and Expression Profile Analysis of Heat Shock Transcription Factors in Mungbean. Front Genet 2019; 9:736. [PMID: 30687395 PMCID: PMC6336897 DOI: 10.3389/fgene.2018.00736] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/22/2018] [Indexed: 11/30/2022] Open
Abstract
Heat shock transcription factors (Hsfs) are essential elements in plant signal transduction pathways that mediate gene expression in response to various abiotic stresses. Mungbean (Vigna radiata) is an important crop worldwide. The emergence of a genome database now allows for functional analysis of mungbean genes. In this study, we dissect the mungbean Hsfs using genome-wide identification and expression profiles. We characterized a total of 24 VrHsf genes and classified them into three groups (A, B, and C) based on their phylogeny and conserved domain structures. All VrHsf genes exhibit highly conserved exon-intron organization, with two exons and one intron. In addition, all VrHsf proteins contain 16 distinct motifs. Chromosome location analysis revealed that VrHsf genes are located on 8 of the 11 mungbean chromosomes, and that seven duplicated gene pairs had formed among them. Moreover, transcription patterns of VrHsf genes varied in different tissues, indicating their different roles in plant growth and development. We identified multiple stress related cis-elements in VrHsf promoter regions 2 kb upstream of the translation initiation codons, and the expression of most VrHsf genes was altered under different stress conditions, suggesting their potential functions in stress resistance pathways. These molecular characterization and expression profile analyses of VrHsf genes provide essential information for further function investigation.
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Affiliation(s)
- Shuai Li
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Runhao Wang
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hanqi Jin
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yanhua Ding
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunmei Cai
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Jex AR, Gasser RB, Schwarz EM. Transcriptomic Resources for Parasitic Nematodes of Veterinary Importance. Trends Parasitol 2018; 35:72-84. [PMID: 30529253 DOI: 10.1016/j.pt.2018.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/17/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022]
Abstract
Parasitic nematodes are important pathogens of animals, causing diseases that impact on agricultural production worldwide. Research on these worms has been constrained by a lack of genetic and genomic tools. Nonetheless, over the past decade this field has made substantial advances, many of which have been led by transcriptomic sequencing. The present review summarises major transcriptomic studies of veterinary parasitic nematodes in recent years, and comments on overarching themes stemming from this work that inform our understanding of parasitism. Finally, we comment on current, state-of-the-art informatic tools for the analysis of complex worm transcriptomes to extract maximum the molecular information from them.
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Affiliation(s)
- Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Erich M Schwarz
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Cornell University, Ithaca, NY 14850, USA
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Rödelsperger C, Meyer JM, Prabh N, Lanz C, Bemm F, Sommer RJ. Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus. Cell Rep 2018; 21:834-844. [PMID: 29045848 DOI: 10.1016/j.celrep.2017.09.077] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/01/2017] [Accepted: 09/24/2017] [Indexed: 01/24/2023] Open
Abstract
The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P. pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P. pacificus. Despite widespread conservation of synteny between P. pacificus and C. elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C. elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P. pacificus.
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Affiliation(s)
- Christian Rödelsperger
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
| | - Jan M Meyer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Neel Prabh
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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21
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Lilley CJ, Maqbool A, Wu D, Yusup HB, Jones LM, Birch PRJ, Banfield MJ, Urwin PE, Eves-van den Akker S. Effector gene birth in plant parasitic nematodes: Neofunctionalization of a housekeeping glutathione synthetase gene. PLoS Genet 2018; 14:e1007310. [PMID: 29641602 PMCID: PMC5919673 DOI: 10.1371/journal.pgen.1007310] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/26/2018] [Accepted: 03/16/2018] [Indexed: 11/24/2022] Open
Abstract
Plant pathogens and parasites are a major threat to global food security. Plant parasitism has arisen four times independently within the phylum Nematoda, resulting in at least one parasite of every major food crop in the world. Some species within the most economically important order (Tylenchida) secrete proteins termed effectors into their host during infection to re-programme host development and immunity. The precise detail of how nematodes evolve new effectors is not clear. Here we reconstruct the evolutionary history of a novel effector gene family. We show that during the evolution of plant parasitism in the Tylenchida, the housekeeping glutathione synthetase (GS) gene was extensively replicated. New GS paralogues acquired multiple dorsal gland promoter elements, altered spatial expression to the secretory dorsal gland, altered temporal expression to primarily parasitic stages, and gained a signal peptide for secretion. The gene products are delivered into the host plant cell during infection, giving rise to "GS-like effectors". Remarkably, by solving the structure of GS-like effectors we show that during this process they have also diversified in biochemical activity, and likely represent the founding members of a novel class of GS-like enzyme. Our results demonstrate the re-purposing of an endogenous housekeeping gene to form a family of effectors with modified functions. We anticipate that our discovery will be a blueprint to understand the evolution of other plant-parasitic nematode effectors, and the foundation to uncover a novel enzymatic function.
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Affiliation(s)
- Catherine J. Lilley
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Abbas Maqbool
- Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Duqing Wu
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Hazijah B. Yusup
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Laura M. Jones
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Paul R. J. Birch
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark J. Banfield
- Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Peter E. Urwin
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sebastian Eves-van den Akker
- Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
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22
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Hunt VL, Hino A, Yoshida A, Kikuchi T. Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level. Sci Rep 2018; 8:5192. [PMID: 29581469 PMCID: PMC5979966 DOI: 10.1038/s41598-018-23514-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/14/2018] [Indexed: 12/02/2022] Open
Abstract
Strongyloides spp., gastrointestinal nematode parasites of humans and other animals, have genetically identical parasitic and free-living adult life cycle stages. This is an almost unique feature amongst nematodes and comparison of these two stages can provide insights into the genetic basis and evolution of Strongyloides nematode parasitism. Here, we present RNAseq data for S. venezuelensis, a parasite of rodents, and identify genes that are differentially expressed in parasitic and free-living life cycle stages. Comparison of these data with analogous RNAseq data for three other Strongyloides spp., has identified key protein-coding gene families with a putative role in parasitism including WAGO-like Argonautes (at the genus level) and speckle-type POZ-like coding genes (S. venezuelensis-S. papillosus phylogenetic subclade level). Diverse gene families are uniquely upregulated in the parasitic stage of all four Strongyloides species, including a distinct upregulation of genes encoding cytochrome P450 in S. venezuelensis, suggesting some diversification of the molecular tools used in the parasitic life cycle stage among individual species. Together, our results identify key gene families with a putative role in Strongyloides parasitism or features of the parasitic life cycle stage, and deepen our understanding of parasitism evolution among Strongyloides species.
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Affiliation(s)
- Vicky L Hunt
- Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Akina Hino
- Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
- Department of Environmental Parasitology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Akemi Yoshida
- Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Taisei Kikuchi
- Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
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23
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Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation. G3-GENES GENOMES GENETICS 2018; 8:353-362. [PMID: 29162683 PMCID: PMC5765362 DOI: 10.1534/g3.117.300281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Reproductive proteins are often observed to be the most rapidly evolving elements within eukaryotic genomes. The major sperm protein (MSP) is unique to the phylum Nematoda and is required for proper sperm locomotion and fertilization. Here, we annotate the MSP gene family and analyze their molecular evolution in 10 representative species across Nematoda. We show that MSPs are hyper-conserved across the phylum, having maintained an amino acid sequence identity of 83.5–97.7% for over 500 million years. This extremely slow rate of evolution makes MSPs some of the most highly conserved genes yet identified. However, at the gene family level, we show hyper-variability in both gene copy number and genomic position within species, suggesting rapid, lineage-specific gene family evolution. Additionally, we find evidence that extensive gene conversion contributes to the maintenance of sequence identity within chromosome-level clusters of MSP genes. Thus, while not conforming to the standard expectation for the evolution of reproductive proteins, our analysis of the molecular evolution of the MSP gene family is nonetheless consistent with the widely repeatable observation that reproductive proteins evolve rapidly, in this case in terms of the genomic properties of gene structure, copy number, and genomic organization. This unusual evolutionary pattern is likely generated by strong pleiotropic constraints acting on these genes at the sequence level, balanced against expansion at the level of the whole gene family.
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Holz A, Streit A. Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae. Genome Biol Evol 2017; 9:2826-2843. [PMID: 29036592 PMCID: PMC5737618 DOI: 10.1093/gbe/evx197] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small noncoding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies. We characterized the small RNAs of two developmental stages of three different Strongyloididae species and compared them with the well-studied free-living nematodes Caenorhabditis elegans and Pristionchus pacificus. Strongyloididae have conserved and taxon-specific microRNAs, many of which are differentially regulated between the two developmental stages. We identified a novel class of around 27-nucleotide-long RNAs starting with 5'G or A, of which a large fraction have the potential to target transposable elements. These RNAs most likely have triphosphates at their 5' ends and are therefore presumably synthesized by RNA-dependent RNA polymerases. In contrast to C. elegans but similarly to some other nematode taxa, Strongyloididae have no Piwi-interacting RNAs, nor do their genomes encode Argonaute proteins of the Piwi family. Finally, we attempted but failed to detect circulating parasite small RNAs in the blood of hosts.
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Affiliation(s)
- Anja Holz
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Adrian Streit
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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